ARTICLE DOI: 10.1038/s41467-017-01173-4 OPEN YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer Wenyi Mi 1,2, Haipeng Guan3,4, Jie Lyu 5, Dan Zhao3,4, Yuanxin Xi5, Shiming Jiang1,2, Forest H. Andrews6, Xiaolu Wang1,2, Mihai Gagea 7, Hong Wen1,2, Laszlo Tora 8,9,10,11, Sharon Y.R. Dent1,2,12, Tatiana G. Kutateladze6, Wei Li 5, Haitao Li 3,4 & Xiaobing Shi 1,2,12 Recognition of modified histones by “reader” proteins constitutes a key mechanism reg- ulating diverse chromatin-associated processes important for normal and neoplastic devel- opment. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively tran- scribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis. 1 Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA. 2 Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA. 3 MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. 4 Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China. 5 Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA. 6 Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. 7 Department of Veterinary Medicine & Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA. 8 Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France. 9 Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France. 10 Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France. 11 Université de Strasbourg, 67404 Illkirch, France. 12 Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. Wenyi Mi, Haipeng Guan, Jie Lyu and Dan Zhao contributed equally to this work. Correspondence and requests for materials should be addressed to W.L. (email: [email protected]) or to H.L. (email: [email protected]) or to X.S. (email: [email protected]) NATURE COMMUNICATIONS | 8: 1088 | DOI: 10.1038/s41467-017-01173-4 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01173-4 ysine acetylation is one of the most frequent post- ovarian serous cystadenocarcinoma (27%), and head and Ltranslational modifications occurring on histones that play neck squamous cell carcinoma (23%) (Fig. 1a). Importantly, a critical role in regulating chromatin dynamics and the YEATS2 gene expression levels are positively correlated to its accessibility of the underlying DNA in eukaryotes1. Acetylation amplification status in these tumors (Supplementary Fig. 1b–d). on histone lysine residues is controlled by two families of coun- In human NSCLC and ovarian cancer patients, high YEATS2 teracting enzymes: histone acetyltransferases (HATs) and histone expression levels are correlated with worse prognosis (Supple- deacetylases (HDACs), and is normally associated with active mentary Fig. 1e, f). transcription2, 3. In addition to neutralizing the positive charge on We next assessed YEATS2 expression levels across a number of the side chain of lysine residues, the bulky acetyl groups can also lung cancer cell lines. Compared to the immortalized “normal” serve as docking sites for reader proteins, which recognize this lung fibroblast cell lines (WI-38 and IMR-90), YEATS2 was specific modification and transduce the molecular signals to elicit overexpressed at both transcript and protein levels in all NSCLC various downstream biological outcomes4. Bromodomain (BRD) cell lines we examined (Fig. 1b and Supplementary Fig. 2a). has long been thought to be the sole protein module that speci- YEATS2 is a stoichiometric component of the ATAC HAT fically recognizes acetyllysine motifs5. Some tandem plant complex, which catalyzes histone acetylation, mainly on H3K9 homeodomain zinc fingers were later found to bind histone H3 in and H3K14, by the enzymatic subunit GCN5 or PACF12, 13. – an acetylation-sensitive manner6 8. Recently, we identified the Interestingly, compared with the immortalized normal cells, we YEATS domain of AF9 protein as a novel reader of histone also observed elevated levels of GCN5 and PCAF in most acetylation9. YEATS domain is evolutionarily conserved from examined lung cancer cells (Fig. 1b), suggesting that essential yeast to human10. There are four YEATS domain-containing subunits of the ATAC complex cooperate in human cancers likely proteins in humans and three in Saccharomyces cerevisiae11. All leading to an super-active complex. Consistent with this the YEATS domain proteins are associated with chromatin- speculation, we found global histone acetylation levels, especially associated complexes, such as HAT complexes and chromatin- H3K9ac, were evidently higher in the NSCLC cell lines than the remodeling complexes, however, the functions of these proteins, immortalized normal cells (Fig. 1b). Interestingly, we also and particularly their YEATS domains, are not well understood. observed increased HDAC1 protein levels in cancer cells, which YEATS domain-containing 2 (YEATS2) is a scaffolding sub- is opposite to the increased K9 acetylation (Fig. 1b). unit of the Ada-two-A-containing (ATAC) complex, a conserved Even though cancer cells acquire multiple genetic and metazoan HAT complex12, 13. Vertebrate ATAC complexes share epigenetic abnormalities, their growth and survival are often the same catalytic HAT subunit, GCN5, or the highly related impaired by inactivation of a single oncogene. Since YEATS2 is PCAF in mammals, with another multi-subunit complex highly amplified in NSCLC, we sought to determine whether Spt–Ada–Gcn5–acetyltransferase (SAGA)14, 15. Although the depletion of YEATS2 affects lung cancer cell growth. To this end, SAGA complex has been extensively studied in both yeast and we knocked down (KD) YEATS2 gene expression in the H1299 humans, much less is known about the ATAC complex. GCN5 lung adenocarcinoma cell line using two independent shRNAs and PCAF in the ATAC complex mainly acetylate histone H3K9 (Supplementary Fig. 2b) and determined cell growth. We and H3K14, while the second acetyltransferase ATAC2 in the observed a marked suppression of cell proliferation in cells complex has been reported to modify H4K1616, 17. The ATAC treated with YEATS2-targeting shRNAs (shY2) compared with complex occupies distinct set of genes from SAGA and coordi- the cells treated with a non-targeting control shRNA (shNT) nates MAP kinases to regulate JNK target genes18, 19. The sub- (Fig. 1c). Notably, the levels of suppression were correlated with units of SAGA form four sub-modules that exert distinct the KD efficiency, with severe growth defect observed in the cells molecular functions within the complex20, 21, however, within the with higher KD efficiency. The growth inhibition by YEATS2 KD ATAC complex, except the HAT module, the functions of most was also observed in additional NSCLC cell lines (A549, H520, other subunits remain largely unknown. In this study, we char- and Ludlu-1) and ovarian cancer cell lines (CaoV3 and HeyA8) acterized the molecular and biological functions of YEATS2 that also harbor YEATS2 amplification, as well as in the within the ATAC complex. We found that the YEATS2 gene is immortalized normal lung fibroblast cells (WI-38 and IMR-90) highly amplified in human cancers including non-small cell lung that do not have YEATS2 overexpression (Supplementary cancer (NSCLC). Depletion of YEATS2-reduced cancer cell Fig. 2c–i), suggesting that YEATS2 is an essential gene for a growth, survival and transformation activity. The YEATS domain broad range of cancer cell lines as well as non-cancerous cells. of YEATS2 binds to acetylated histone H3K27 (H3K27ac). Cancer cells evolve with capability to undergo unlimited cell Recognition of histone acetylation is important for the functions division and transformation. We next sought to test whether of YEATS2 in cells. Disruption of acetylation recognition of YEATS2 is required for cell survival and transformation of YEATS2-abrogated GCN5/PCAF-mediated promoter histone NSCLC. In clonogenic assay of both H1299 and A549 cells, the acetylation and consequently, suppressed the expression of its YEATS2 KD cells developed fewer colonies compared with the target genes, including the ribosomal protein-encoding genes that control cells, suggesting that YEATS2 is required for lung cancer are essential for cell growth and survival. Taken together, our cell survival